[Bio] / FortyEight / rp_make_PHOBIUS_attributes.pl Repository:
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Diff of /FortyEight/rp_make_PHOBIUS_attributes.pl

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revision 1.2, Thu Oct 11 20:16:03 2007 UTC revision 1.3, Wed Oct 17 15:32:50 2007 UTC
# Line 2  Line 2 
2  my $genome = shift(@ARGV);  my $genome = shift(@ARGV);
3  my $date = localtime();  my $date = localtime();
4    
5  opendir(DIR,$jobdir."/$genome");  opendir(DIR,$jobdir."/rp/$genome");
6    
7  if(! -d "$jobdir/rp/$genome/attributes"){  if(! -d "$jobdir/rp/$genome/attributes"){
8      `mkdir $jobdir/rp/$genome/attributes`;      `mkdir $jobdir/rp/$genome/attributes`;
# Line 16  Line 16 
16  foreach my $file (@files){  foreach my $file (@files){
17      if ($file =~/($genome.peg.\d+).PHOBIUS_result/){      if ($file =~/($genome.peg.\d+).PHOBIUS_result/){
18          my $peg = "fig|".$1;          my $peg = "fig|".$1;
19          open(IN,$jobdir."/$genome/$file");          open(IN,$jobdir."/rp/$genome/$file");
20          my @tm_locations = ();          my @tm_locations = ();
21          while ($_ = <IN>){          while ($_ = <IN>){
22              if($_ =~/SIGNAL\s+(\d+)\s+(\d+)/){              if($_ =~/SIGNAL\s+(\d+)\s+(\d+)/){
# Line 37  Line 37 
37    
38  close(PHOB);  close(PHOB);
39    
40  `rm $jobdir/$genome/*.PHOBIUS_result`;  `rm $jobdir/rp/$genome/*.PHOBIUS_result`;

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